Electron Backscatter Diffraction (EBSD) was used to determine microstructural evolution in AA6082-T6 welds processed by the Bobbin Friction Stir Welding (BFSW). This revealed details of grain-boundaries in different regions of the weld microstructure. Different polycrystalline transformations were observed through the weld texture. The Stirring Zone (SZ) underwent severe grain fragmentation and a uniform Dynamic Recrystallisation (DRX). The transition region experienced stored strain which changed the grain size and morphology via sub-grain-boundary transformations. Other observations were of micro-cracks, the presence of oxidization, and the presence of strain hardening associated with precipitates. Flow-arms in welds are caused by DRX processes including shear, and low and high angle grain boundaries. Welding variables affect internal flow which affects microstructural integrity. The shear deformation induced by the pin causes a non-uniform thermal and strain gradient across the weld region, leading to formation of mixed state transformation of grain morphologies through the polycrystalline structure. The grain boundary mapping represents the differences in DRX mechanism I different regions of the weld, elucidates by the consequences of the thermomechanical nature of the weld. The EBSD micrographs indicated that the localised stored strain at the boundary regions of the weld (e.g. flow-arms) has a more distinct effect in emergence of thermomechanical nonuniformities within the DRX microstructure.